[fMRIPost-AROMA] fMRIPost-AROMA sets Repetition Time to 1.0

Software Support
1

Summary of what happened:

My TR is 1.5 sec, but after running fMRIpost-AROMA, it is set to 1.0 sec.

Command used:

  docker run --rm -it \
    -v "${FMRIPREP_DIR}:/prep:ro" \
    -v "${AROMA_DIR}:/out" \
    -v "${WORK_DIR}/${PROCESS}:/work" \
    nipreps/fmripost-aroma:main \
    /prep /out participant \
    --skip_bids_validation \
    --participant-label ${PNUM} \
    --task-id ${TASK} \
    --denoising-method nonaggr \
    --melodic-dimensionality 20 \
    --nprocs 8 \
    --omp-nthreads 2 \
    --mem 24000 \
    --notrack \
    -w /work

Version:

fMRIPost-AROMA version 0.1.11
fmriprep 24.0.1

Environment (Docker, Singularity / Apptainer, custom installation):

Ubuntu 20.04.6 LTS, Docker 4.33.0

Data formatted according to a validatable standard? Please provide the output of the validator:

Relevant log outputs (up to 20 lines):

~/mridata/rvh/derivatives/fmriprep/sub-128/func$ 3dinfo -tr sub-128_task-rvh_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz 
1.500000

~/mridata/rvh/derivatives/aroma/sub-128/func$ 3dinfo -tr sub-128_task-rvh_run-01_space-MNI152NLin6Asym_res-2_desc-nonaggrDenoised_bold.nii.gz 
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /home/mkkim11/mridata/rvh/derivatives/aroma/sub-128/func/sub-128_task-rvh_run-01_space-MNI152NLin6Asym_res-2_desc-nonaggrDenoised_bold.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
1.000000

Hi,

I am having trouble with using fMRIpost-AROMA. My sequence has TR that is longer than 1.0 sec, and fMRIpost-AROMA sets it to 1.0 and I can’t run GLM or other analyses due to the timing mismatch results from this. What can I do? Thank you in advance.

2

For now, I am adding this quick fix after running AROMA

  for run in ${RUNS}; do
    fslcpgeom \
      ${FMRIPREP_DIR}/sub-${PNUM}/func/sub-${PNUM}_task-${TASK}_run-${run}_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz \
      ${AROMA_DIR}/sub-${PNUM}/func/sub-${PNUM}_task-${TASK}_run-${run}_space-MNI152NLin6Asym_res-2_desc-nonaggrDenoised_bold.nii.gz
  done
3

That looks like a bug in fMRIPost-AROMA. I’ve opened an issue (TR is not set in denoised BOLD files · Issue #119 · nipreps/fmripost-aroma · GitHub) and I’ll try to fix it for the next release. Thanks for reporting!

4

Sounds great, I look forward to the update. Thank you for a great software.

5

Can you try the updated nipreps/fmripost-aroma:main Docker image and see if the TR is correct now?

6

Thanks, it works now!